The Mississippi state flag and US flag fly in the Circle on campus at the University of Mississippi in Oxford, Miss., Oct. 16. The state flag was removed Monday, days after the student senate, the faculty senate, and other groups adopted a student-led resolution calling for removal of the banner from campus.

The University of Mississippi removed the state flag on its main campus on Monday morning because the banner design includes the Confederate battle emblem, which has come under fire in recent months for symbolizing slavery and segregation.

A student-led resolution had been calling for the removal of the flag, and the removal finally came days after the student senate, the faculty senate, and other groups adopted the resolution. The flag will now be sent to the university’s archives, according to Interim Chancellor Morris Stocks.

Over 200 people had taken part in a remove-the-flag rally on Oct. 16, sponsored by the university chapter of the NAACP.

"As Mississippi's flagship university, we have a deep love and respect for our state," Mr. Stocks said in a statement Monday. "I understand the flag represents tradition and honor to some. But to others, the flag means that some members of the Ole Miss family are not welcomed or valued."

The flag became a lightning rod for controversy in June when a white gunman massacred nine black worshippers during bible study in Charleston, S.C. Police say the attack was racially motivated, and the gunman had been photographed posing in front of the flag. Since the shooting, the flag and other symbols of the Confederacy have been removed from public display across the South.

Writing for The Christian Science Monitor a week after the Charleston massacre, Patrik Jonsson said that the Confederate legacy, once "set in stone" in the South, is now "up for debate like never before."

"Almost overnight, Americans are deeply questioning the role and permanence of state-sanctioned symbols of a past regime founded on white supremacy in a present multiethnic and pluralistic society," writes Mr. Jonsson.

The Mississippi state flag has featured the Confederate battle emblem since 1894, and a statewide vote in 2001 saw Mississippians choose to keep the flag.

However, the University of Mississippi, also known as Ole Miss, has been slowly phasing out Old South symbolism from its campus for decades. Several years ago the university retired the Colonel Rebel mascot – a white-haired old man some thought resembled a plantation owner. Nearly 20 years ago the university banned sticks from the football stadium, which prevented most fans bringing Confederate battle flags to games.

"The University of Mississippi community came to the realization years ago that the Confederate battle flag did not represent many of our core values, such as civility and respect for others," Stocks said in his statement on Monday. "Since that time, we have become a stronger and better university. We join other leaders in our state who are calling for a change in the state flag."

Since the Charleston shootings several cities and counties in the state have stopped flying the flag. Three historically black colleges in the state had already stopped flying the flag, and Democrat Bennie Thompson, Mississippi's only black US representative, does not display the flag in his offices.

There is some opposition to the removal of the flag. A Change.org petition to keep the flag had almost 1,800 signatures at noon on Monday. The petition calls on university students and Mississippians to "rise up and push back on political correctness and support the state flag."

"In order to live in a free society, the possibility to be offended will occasionally occur," the petition adds. "Removing symbols, flags, and monuments will do nothing to change the way people feel in their hearts."

Gibbs Knotts, a political scientist at the University of Charleston in South Carolina, told Jonsson that there is "some validity" to the argument that Confederate symbols are part of Southern heritage and thus deserving of preservation, but he noted that 30 percent of the regional population are also "highly offended" by the flag.

"True, you can't restrict somebody’s free speech," he added, "but you can say that as a government or a state we're not going to put it in a prominent place given how it’s being used by [hate groups] and the fear it brings to a large portion of our population."